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 <p>
This page is part of the <a href="spec_1.53E.jsp">DAS 1.53E specification</a>
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 <h2>Documentation DAS structure service</h2>


<hr>

<h3><a name="structure"/>Retrieve 3D coordinates</h3>
  <br/>

<b>Version:</b> May 11th, 2006

<br/>
<a name="authors"/>
<b>Authors:</b> <a href="mailto:ap3@sanger.ac.uk">Andreas Prlic</a>, Rob Finn, Thomas Down, Tim Hubbard

<br/>

<b>Used by DAS client:</b>

<a href="http://www.dasregistry.org/spice/">
<img src="http://www.dasregistry.org/spice/spice_white_46x15.gif" alt="SPICE"></a>

<br/>

<a name="references"/>
<b>References</b>
<br/>
<div id="reference">
<strong>Adding some SPICE to DAS</strong><br>
<b>Andreas Prlic, Thomas A. Down  and Tim J. P. Hubbard</b><br>
<a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/21/suppl_2/ii40?ijkey=3qeaoju2KiLPOjC&amp;keytype=ref">Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41</a><br>
[<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/suppl_2/ii40">abstract</a>]
[<a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/21/suppl_2/ii40">pdf</a>]
[<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&amp;db=pubmed&amp;list_uids=16204122&amp;dopt=Abstract">pubmed</a>] 
</div>
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<jsp:include page="reference.jsp"/>
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<b>Scope:</b> Reference servers.

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<b>Command:</b> <i>structure</i>

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<b>Format:</b>
<pre>

<i>PREFIX</i>/das/structure?query=structureID[&amp;chain=chainID&amp;model=modelNumb&amp;range=RANGE]

</pre>
<br/>

<b>Description:</b> This query returns coordinates for 3D objects.
<br/>
<b>Arguments:</b>

<%@ include file="sangertablestart.jsp" %>
<table>



	<tr id="row1"><td><b>query</b> (required; one) the id of the object to return. 
	</td><td> e.g. PDB-id , SCOP domain id, etc.</td></tr>
	
	<tr id="row2"><td><b>chain</b> (optional; one or more) the <i>chainID</i> to return.

	</td><td> if the query <i>structureID</i> consists of several
	chains only selected chains are returned. if it is omitted
	all available chains are returned.
	</td></tr>
	
	<tr id="row1"><td><b>model</b> (optional; one or more) the <i>modelNum</i> to return.
	</td><td> if the query <i>structureID</i> has been resolved using
	NMR, several alternate models are available. using this
	argument it is possible to request only individual models.  If
	it is omitted, all available models are returned.
	</td></tr>
	
	<tr id="row2"><td><b>range</b> (optional;)  </td>
	
	<td>this can be provided to request a
	particular range of a PDB structure. The RANGE is defined by
	<pre>start:stop</pre>

	 where both start and stop are defined as consisting of:
	<pre>pdbresnum_insertionCode.chainId</pre> where the
	<i>pdbresnum</i> is mandator and <i>insertionCode</i> and
	<i>chainId</i> are optional. The <b>.</b> and
	<b>_</b>characters are used as separators.  

	examples for valid ranges:

	<pre>?query=5pti&range=15:30</pre>

	<pre>?query=1h4w&range=200.A:221_A.A</pre>
	</td></tr>
	

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<h4>Response:</h4>



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The response to the <i>structure</i> command is the "DASSTRUCTURE" XML-formatted document:



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<b>Format:</b>
<blockquote>



<pre>
&lt;?xml version="1.0" standalone="no"?&gt;
&lt;dasstructure xmlns="http://www.efamily.org.uk/xml/das/2004/06/17/dasstructure.xsd" xmlns:data="http://www.efamily.org.uk/xml/data/2004/06/17/dataTypes.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.efamily.org.uk/xml/das/2004/06/17/dasstructure.xsd" &gt;

	&lt;object dbAccessionId="someid" objectVersion="version" type="objectType" dbSource="someSouce" dbVersion="version" dbCoordSys="coords"  &gt;			
	&lt;/object&gt;

	&lt;objectDetail dbSource="someSouce" property="property"&gt;
			<i>some details about the object. e.g. description, etc.</i> 
	&lt;/objectDetail&gt; 

	&lt;chain id="chainID" model="modelNr" SwissprotId="accessionCode"&gt;	
		&lt;group name="groupName" type="groupType" groupID="groupID" insertCode="iCode"&gt;
			&lt;atom x="xCoord" y="yCoord" z="zCoord" atomName="atomname" atomID="atomID" occupancy="occupancy" tempFactor="tempFactor" altLoc="altLoc"/&gt;
		&lt;/group&gt;

	&lt;/chain&gt;

	&lt;connect type="connectionType" atomSerial="atomID" &gt;
		&lt;atomID atomID="atomID"/&gt;
	&lt;/connect&gt;
	
&lt;/dasstructure>


</pre>
</blockquote>

<%@ include file="sangertablestart.jsp" %>
<table>
<tr id="row1">


   <!-- start of object -->
<tr id="row1"><td>Element:&lt;<b>object</b>&gt; </td>
  <td>(required)
   A description of the structure object. </td></tr>
   

   <tr id="row1"><td>Attributes:</td><td></td></tr>


   <tr id="row1"><td>attribute:objectVersion</td>
   <td> (required) version of Object. e.g. MD5 checksum for protein sequences.</td>
	</tr>
	
     <tr id="row1"><td>attribute:type</td>
   <td> (optional) a type for this object.e.g. DNA, PROTEIN, STRUCTURE, etc. </td>
	</tr>
	
    <!-- start dbRef -->
	<tr id="row1"><td>attributeGroup:dbRef</td>
	<td>This attribute group is used for referring to a database.</td></tr>
	
	<tr id="row1"><td>attribute:dbSource</td>
	<td>(required).  The name of the database.</td>
	</tr>

	<tr id="row1"><td>attribute:dbVersion</td>
	<td>(required).  The version of the database.</td>
	</tr>
	
	<tr id="row1"><td>attribute:dbCoordSys</td>
	<td>(optional).  The co-ordinate system of used by the database.  This is not always the same as the database.  For example, Pfam uses UniProt as an underlying co-ordinate system.  
	</td></tr>
	
	<tr id="row1"><td>attribute:dbAccessionId</td>
	
	<td>(required).  The database entry accession id.  For example, SCOP have sunid, Pfam accessions(PF01020).
	</td></tr>


    <!-- end dbRef -->

    
   <!-- end of object -->

   <tr id="row2"><td>Element:&lt;<b>objectDetail</b>&gt; </td> 
	<td>(optional; zero or more) details about the object</td>
	</tr>

   <!-- begin of detail.inc-->   
	<tr id="row2"><td>attributeGroup:detail</td>
	<td>The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.
	</td></tr>
	<tr id="row2"><td>attribute:dbSource</td><td>(required). The database where the information about this source orginates.</td></tr>
	<tr id="row2"><td>attribute:property</td><td>(required). A description of the CDATA.  For example, if you wanted to give an alternative id for a database, e.g. a UniProt ID , then the 
	&lt;someDetail dbSource="UniProt" property="id"&gt;P50225&lt;/someDetail&gt;
	</td></tr>
<!-- end of detail.inc-->




   <tr id="row1"><td>Element:&lt;<b>chain</b>&gt;</td>
  <td> (zero or more) groups everything that belongs to a chain.</td>
  </tr>
    <tr id="row1"><td>Attributes:</td><td></td></tr>

   <tr id="row1"><td>attribute:id</td>
   <td> (required)  is the Identifier for this chain, e.g. "A","B" </td>
	</tr>
	
   <tr id="row1"><td>attribute:model</td>
   <td>  (optional) if the structure is an NMR structure, this gives the model number of the current chain. </td>
   </tr>

   <tr id="row1"><td>attribute:SwissProtId</td>
   <td>  (optional) SwissProt accession code that is related to this chain </td>
   </tr>
  
   <tr id="row2"><td>Element:&lt;<b>group</b>&gt;</td>
   <td>(optional;) a group of atoms.
    e.g. representing an amino acid or a hetero molecule.
	</td></tr>
   <tr id="row2"><td>attribute:type</td> 
   <td> (required) the type of the group. e.g. amino,
   nucleotide, hetatom.  </td>
	</tr>
	<tr id="row2"><td>attribute:name</td> 
   <td> (required) the name of the group. e.g. ALA</td>
	</tr>
	
	
   <tr id="row2"><td>attribute:groupID</td> 
   <td>(required) the PDB code of the amino acid. e.g. 25,26,27A</td>
   </tr>
   <tr id="row2"><td>attribute:insertCode</td> 
   <td>(optional) insertion code for amino acid. e.g 86A, 86B</td>
	</tr>
	
	
	
   <tr id="row1"><td>Element:&lt;<b>atom</b>&gt;</td>
  <td> (required; one or more) a single atom.</td>
	</tr>
	
   <tr id="row1"><td>Attributes:</td><td></td></tr>

   <tr id="row1"><td>attribute:x, attribute:y, attribute:z</td>
   <td> required) the coordinates of the atom.</td>
	</tr>
	
   <tr id="row1"><td>attribute:atomName</td>
   <td> (required) The PDB file notation is used. e.g. " N  "</td>
	</tr>
   
   <tr id="row1"><td>attribute:atomID</td>
   <td> (required) PDB number of atom. e.g. 148,149,150A,151B</td>
	</tr>
	
   <tr id="row1"><td>attribute:occupancy</td>
   <td> (optional) Occupancy.</td>
	</tr>

   <tr id="row1"><td>attribute:tempFactor</td>

   <td> (optional) Temperature factor.</td>
	</tr>
   <tr id="row1"><td>attribute:altLoc</td>
   <td> (optional) the PDB alternate location field.</td>
   </tr>
   


   <tr id="row2"><td>Element:&lt;<b>connect</b>&gt;</td>
  <td> (optional) connectivity between atoms.
  for amino acids the connectivity is not needed, but for HET it
   is mandatory, otherwise a viewer would not know how to display them.
   
   </td>
   </tr>
   <tr id="row2"><td>attribute:type</td>

   <td>the type of bond</td>
	</tr>
   <tr id="row2"><td>attribute:atomSerial</td>
   <td>serial number of the atom the connect information refers to .</td>
	</tr>
	
   <tr id="row1"><td>Element:&lt;<b>atomID</b>&gt;</td>
  <td> an atom that is connected to the one specified by this connection.
	</td></tr>
   <tr id="row1"><td>attribute:atomID</td>

   <td>serial number of the atoms.</td>
	</tr>

   

</table>
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<b>Example Responses</b>

<ul>
<li> <a href="http://das.sanger.ac.uk/das/structure/structure?query=1a4a">1a4a structure</a>

</ul>

<hr>

<br/>

The SPICE DAS client for protein structures can be accessed at:

<br/>
<a href="http://www.dasregistry.org/spice/">
<img src="http://www.dasregistry.org/spice/spice_white_46x15.gif"> http://www.dasregistry.org/spice/</a>





    
</div>

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